Proteomic research is the study of all proteins in an organism and is expected to lead to discoveries leading to improved diagnosis and treatment of disease. One problem inherent in proteomics research is the requirement of a high throughput analysis of a large number of proteins. The most widely used protein analysis method is based on 2-D gel electrophoresis and mass spectrometry in which proteins are first separated on gels according to charge and size, and then identified by mass spectrometers. An alternative analysis method is based on isotopic labeling such as isotope-coded affinity tags (ICAT) and tandem mass spectrometry in which no protein separation is needed. Another analysis method is based on protein chips in which thousands of “bait” proteins such as antibodies are immobilized in an array format onto specially treated surfaces. Compared to the other two methods, protein chips have the advantage of being scalable, and their organized nature enables high throughput screening using robotic, imaging, or analytical methods. Protein chips are powerful tools for the genome-scale analysis of gene function, such as enzyme activity, protein-protein, protein-DNA, protein-RNA, and protein-ligand interactions, directly on the protein level. The main limitation in developing protein chips is the lack of a universal peptide-binding scaffold to create tailor-made protein capturing reagents that specifically bind to every single protein in a given organism.
Because of their high specificity and affinity to proteins, monoclonal antibodies have been widely considered for use as protein capturing reagents of choice for protein chips. Several antibody-based low-density protein chips have been developed. However, generation of specific antibodies for each protein remains a time-consuming and expensive challenge. In particular, the preparation of monoclonal antibodies requires the availability of thousands of purified soluble proteins which are difficult to obtain in large scale. In addition, the stability of immobilized antibodies is a concern. Therefore, non-antibody based protein capturing reagents that can be tailored to specifically bind to a target peptide are desired. Ideally, such reagents should have high stability, similar or better specificity and affinity as antibodies, and the reagents should be able to be prepared on a large scale.